worked on unit tests for sam.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1499 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index 92b8d95bf2d9cfccb14c1b290ed3b040c5b7347e..0161cd7fee757a98194fdc53158811fe9e96ac7b 100644 (file)
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -318,6 +318,11 @@ class Sam < Filesys
       raise SamError, "Bad cigar with internal H: #{cigar}"
     end
 
+    # Check cigar soft clipping only at ends or H.
+    if cigar.gsub(/^[0-9]+H|[0-9]+H$/, "").gsub(/^[0-9]+S|[0-9]+S$/, "").match('S')
+      raise SamError, "Bad cigar with internal S: #{cigar}"
+    end
+
     # Check cigar length matches sequence length.
     unless cigar == '*' or seq == '*'
       cigar_len = 0